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User uploads their paper.pdf, and selects to use creative-commons license, which then adds three cc files to the item. Two of these are internal, but one of the cc-license files is an RDF file which is marked as external, so it will end up showing in the uploaded files section. When the user is working on a submission in progress and goes back to uploads step, they see the cc-licence.rdf file, but not their paper.pdf.
That happens when they have unchecked (this item will have more than one file). Perhaps a simple fix would be to have the upload tab listing all files in the content bundle regardless of what the (this item will have more than one file) says.

IRC chat on June 14 2010
<PeterDietz> I've perhaps hit a side effect of http://jira.dspace.org/jira/browse/DS-295 – CC License incorrect mime type.
<PeterDietz> when user creates an item and they leave unselected (this has multiple files), then they upload their paper, and choose cc-license. Well, when it comes back to them in a workflow, in the uploaded-items tab, it shows some license-rdf as only file, and their pdf paper isn't listed
<PeterDietz> so if they go back and say (this has multiple files), it will then it show all files license-rdf and mypaper.pdf. The reason as my metadata librarian was trying to explain, is that by saying rdf is internal=false, that means its public, thus its shown as an uploaded bitstream to the uploader
<kshepherd> hmm

stuartlewis hmmms too
<PeterDietz> in the end, once its published, its in the cc-license bundle so it doesn't get shown to end user/visitor, but in the interim, the uploader will be like hmm whats this license-rdf file doing
<kshepherd> i don't think the "publicness" is a problem
<kshepherd> it's that silly initial questions step
<PeterDietz> yeah, I would think that the uploaded step should show all bitstreams that are internal=false, regardless of their choice of saying (this has multiple files)
<kshepherd> that could be one fix, indeed..
<kshepherd> "this has multiple files" should be interpreted as "there will be multiple files in the CONTENT/ORIGINAL bundle" by DSpace